Today Python Patches

Package-Manager: portage-2.2.0_alpha23/cvs/Linux x86_64

3 files changed, 225 insertions, 5 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 5d4c5fa9a432..3fb94e24f7ab 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.53 2011/02/02 17:18:02 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.54 2011/02/15 09:01:24 jlec Exp $
+
+*ccpn-2.1.5_p110215 (15 Feb 2011)
+
+  15 Feb 2011; Justin Lecher <jlec@gentoo.org> +ccpn-2.1.5_p110215.ebuild:
+  Today Python Patches
 
 *ccpn-2.1.5_p110202 (02 Feb 2011)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 45dbc6acd4ae..4eb8ca2bf7fa 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -17,14 +17,16 @@ DIST analysis2.1.3_1.tar.gz 18932918 RMD160 5f19ea6fe47c2910d16fcba8d1a78f0e1dea
 DIST analysis2.1.5.tar.gz 20338459 RMD160 b0706c859c1ee4da2ab80ee41534197268f73d44 SHA1 70dc5e6b2752d6b7d5c8673fc992ebd0a88e6ad0 SHA256 9f91f1bd56fb73fd24e71d396c96c0f0d31b92287664b6a2e756f6efc630b31b
 DIST ccpn-update-100806.patch.bz2 187965 RMD160 3297162fe3314aa405ee58737ce45cda084834e5 SHA1 338423d9f36da3fb10dc9d9a3b8aeb932ae3bfd0 SHA256 5cea7899edb96237a6674f04a1beee6ad7b309e12964ea8b25d9ea6ff752d0d4
 DIST ccpn-update-110202.patch.bz2 54603 RMD160 81d4123e155816c372702084a8d1433e256ec365 SHA1 57f4496f51b9e16b1eb5b85dcb332b032e61da97 SHA256 9f2dd2106ceef1fb120ee9d1f5973e2ac8105c260c8e981b429211738747fb02
+DIST ccpn-update-110215.patch.bz2 64294 RMD160 99c8e1a62ac25d7ed088263bbe2f7fb25d9ec0aa SHA1 457391c01c47f66f52813d797a1b293c3db94028 SHA256 e95045f926cc7240e16d61c5663f5fd208a5f27ec76a09a22d80494204678cce
 EBUILD ccpn-2.1.3.1_p100806.ebuild 5190 RMD160 c1dd4e2443ab5cf8386627a9feba25be6e61b715 SHA1 0d9700191a04c6ed5f106e2712b010d499315827 SHA256 ed26ef362193f91d4726fd49a1c4b19c1f975c3847b0616ada2e64ce7a90ffa5
 EBUILD ccpn-2.1.5_p110202.ebuild 5770 RMD160 98c49d481a5a0e28d2f62b303950bab3467c3246 SHA1 2fb5b0d792b4dcfac20f4d11d405104ab5f81129 SHA256 77d1d7239204ffa4247501133996478e13f07b863fdfebe5d4b056089f9e08ba
-MISC ChangeLog 9123 RMD160 28a28e9387d06392631811f98523018ef6884526 SHA1 607acf1aaf25db3fc4df131affe2e9440d3efb44 SHA256 7c1aaa25f8662b6667cbb4df9b08b099c391152f7283df8baf53cebb8d87c002
+EBUILD ccpn-2.1.5_p110215.ebuild 5770 RMD160 561d2b42861e5a8f617abe2aaba214e5499c818c SHA1 9ce50230905664b8e2661f1ccf34274cf4866501 SHA256 ee5480bc247900bd4529007732e8283e13db3368ebc2bd04a6d1289beebc6ea6
+MISC ChangeLog 9257 RMD160 9e4457928d6bbcfbe6aee87eea69a55b274978a2 SHA1 cbf4f07e9d93d24eb935af7aec223f95add931c9 SHA256 9129f5eb0543da7c30d4ad9d2fba6163b5bed64ff97bafbccdc53d23ff9e1300
 MISC metadata.xml 317 RMD160 6e56ad407f163d80504468f6fedcfb35fc31db00 SHA1 30b72b0612b1f91712537d24e3a2407eec50e1dd SHA256 1fb093ab05124dcd078fc93a4aa6f787f5829066e100ed98da8ecf65cece63fb
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diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p110215.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p110215.ebuild
new file mode 100644
index 000000000000..025fc9118825
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.1.5_p110215.ebuild
@@ -0,0 +1,213 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p110215.ebuild,v 1.1 2011/02/15 09:01:24 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2:2.5"
+PYTHON_USE_WITH="ssl tk"
+
+inherit eutils portability python toolchain-funcs versionator
+
+PATCHSET="${PV##*_p}"
+MY_PN="${PN}mr"
+MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
+MY_MAJOR="$(get_version_component_range 1-3)"
+
+DESCRIPTION="The Collaborative Computing Project for NMR"
+SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
+	[[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI}	http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${PATCHSET}.patch.bz2"
+HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="extendnmr +opengl"
+
+RDEPEND="
+	dev-lang/tk[threads]
+	>=dev-python/numpy-1.4
+	>=dev-tcltk/tix-8.4.3
+	=sci-libs/ccpn-data-"${MY_MAJOR}"*
+	x11-libs/libXext
+	x11-libs/libX11
+	opengl? (
+		media-libs/freeglut
+		dev-python/pyglet )"
+# We need to fix this
+#		sci-chemistry/mdd
+DEPEND="${RDEPEND}"
+PDEPEND="
+	extendnmr? (
+		sci-chemistry/aria
+		sci-chemistry/prodecomp )"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
+
+pkg_setup() {
+	python_set_active_version 2
+}
+
+src_prepare() {
+	[[ -n ${PATCHSET} ]] && \
+		epatch "${WORKDIR}"/ccpn-update-${PATCHSET}.patch
+
+	epatch "${FILESDIR}"/${MY_PV}-parallel.patch
+
+	local tk_ver
+	local myconf
+
+	tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
+
+	if use opengl; then
+		GLUT_NEED_INIT="-DNEED_GLUT_INIT"
+		IGNORE_GL_FLAG=""
+		GL_FLAG="-DUSE_GL_TRUE"
+		GL_DIR="${EPREFIX}/usr"
+		GL_LIB="-lglut -lGLU -lGL"
+		GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
+		GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
+
+	else
+		IGNORE_GL_FLAG="-DIGNORE_GL"
+		GL_FLAG="-DUSE_GL_FALSE"
+	fi
+
+	GLUT_NOT_IN_GL=""
+	GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
+
+	rm -rf data model doc license || die
+
+	sed \
+		-e "s:/usr:${EPREFIX}/usr:g" \
+		-e "s:^\(CC =\).*:\1 $(tc-getCC):g" \
+		-e "s:^\(OPT_FLAG =\).*:\1 ${CFLAGS}:g" \
+		-e "s:^\(LINK_FLAGS =.*\):\1 ${LDFLAGS}:g" \
+		-e "s:^\(IGNORE_GL_FLAG =\).*:\1 ${IGNORE_GL_FLAG}:g" \
+		-e "s:^\(GL_FLAG =\).*:\1 ${GL_FLAG}:g" \
+		-e "s:^\(GL_DIR =\).*:\1 ${GL_DIR}:g" \
+		-e "s:^\(GL_LIB =\).*:\1 ${GL_LIB}:g" \
+		-e "s:^\(GL_LIB_FLAGS =\).*:\1 ${GL_LIB_FLAGS}:g" \
+		-e "s:^\(GL_INCLUDE_FLAGS =\).*:\1 ${GL_INCLUDE_FLAGS}:g" \
+		-e "s:^\(GLUT_NEED_INIT =\).*:\1 ${GLUT_NEED_INIT}:g" \
+		-e "s:^\(GLUT_NOT_IN_GL =\).*:\1:g" \
+		-e "s:^\(X11_LIB_FLAGS =\).*:\1 -L${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:^\(TCL_LIB_FLAGS =\).*:\1 -L${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:^\(TK_LIB_FLAGS =\).*:\1 -L${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:^\(PYTHON_INCLUDE_FLAGS =\).*:\1 -I${EPREFIX}/$(python_get_includedir):g" \
+		-e "s:^\(PYTHON_LIB =\).*:\1 $(python_get_library -l):g" \
+		c/environment_default.txt > c/environment.txt
+}
+
+src_compile() {
+	emake -C c all links || die
+}
+
+src_install() {
+	local libdir
+	local tkver
+	local _wrapper
+
+	find . -name "*.pyc" -type d -delete
+
+	libdir=$(get_libdir)
+	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
+
+	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara"
+	use extendnmr && _wrapper="${_wrapper} extendNmr"
+	for wrapper in ${_wrapper}; do
+		sed \
+			-e "s:gentoo_sitedir:${EPREFIX}$(python_get_sitedir):g" \
+		   -e "s:gentoolibdir:${EPREFIX}/usr/${libdir}:g" \
+			-e "s:gentootk:${EPREFIX}/usr/${libdir}/tk${tkver}:g" \
+			-e "s:gentootcl:${EPREFIX}/usr/${libdir}/tclk${tkver}:g" \
+			-e "s:gentoopython:${EPREFIX}/usr/bin/python:g" \
+			-e "s://:/:g" \
+			"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
+		dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
+	done
+
+	local in_path
+	local files
+	local pydocs
+
+	pydocs="$(find python -name doc -type d)"
+	rm -rf ${pydocs} || die
+
+	in_path=$(python_get_sitedir)/${PN}
+
+	for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
+	sed \
+		-e 's:#from __future__:from __future__:g' \
+		-i ${i} || die
+	done
+
+	insinto ${in_path}
+
+	dodir ${in_path}/c
+
+	ebegin "Installing main files"
+		doins -r python || die "main files installation failed"
+	eend
+		dosym ../../../..//share/doc/ccpn-data-${MY_MAJOR}/html ${in_path}/doc || die
+	for i in ${pydocs}; do
+		dosym /usr/share/doc/ccpn-data-${MY_MAJOR}/html/${i} ${in_path}/${i}
+	done
+
+	dosym /usr/share/ccpn/data ${in_path}/data
+	dosym /usr/share/ccpn/model ${in_path}/model
+
+	einfo "Adjusting permissions"
+
+	files="
+		cambridge/c/BayesPeakSeparator.so
+		ccp/c/StructUtil.so
+		ccp/c/StructStructure.so
+		ccp/c/StructBond.so
+		ccp/c/StructAtom.so
+		ccpnmr/c/DyAtomCoord.so
+		ccpnmr/c/DyDistConstraint.so
+		ccpnmr/c/DyDistForce.so
+		ccpnmr/c/AtomCoordList.so
+		ccpnmr/c/DyAtomCoordList.so
+		ccpnmr/c/ContourStyle.so
+		ccpnmr/c/ContourLevels.so
+		ccpnmr/c/SliceFile.so
+		ccpnmr/c/PeakCluster.so
+		ccpnmr/c/Dynamics.so
+		ccpnmr/c/Bacus.so
+		ccpnmr/c/Midge.so
+		ccpnmr/c/DyDistConstraintList.so
+		ccpnmr/c/WinPeakList.so
+		ccpnmr/c/PeakList.so
+		ccpnmr/c/DistConstraint.so
+		ccpnmr/c/CloudUtil.so
+		ccpnmr/c/DistForce.so
+		ccpnmr/c/DistConstraintList.so
+		ccpnmr/c/AtomCoord.so
+		ccpnmr/c/DyDynamics.so
+		ccpnmr/c/ContourFile.so
+		memops/c/ShapeFile.so
+		memops/c/BlockFile.so
+		memops/c/PdfHandler.so
+		memops/c/MemCache.so
+		memops/c/FitMethod.so
+		memops/c/PsHandler.so
+		memops/c/GlHandler.so
+		memops/c/StoreFile.so
+		memops/c/StoreHandler.so
+		memops/c/TkHandler.so"
+	for FILE in ${files}; do
+		fperms 755 ${in_path}/python/${FILE}
+	done
+}
+
+pkg_postinst() {
+	python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+	python_mod_cleanup ${PN}
+}